(a) Describe an experiment that could be used to test whether this is an evolutionary response or phenotypic plasticity.

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1 EEB 2245 Evolutionary Biology Spring 2015 Problem Set 1 1. In a population of 100,000 flour beetles there exists a recessive genetic disease that causes antennae to develop in a Z shape when in the homozygous condition. You find 10 individuals with Z-shaped antennae. Calculate the genotype and allele frequencies for this population of flour beetles. Assume that the population is in Hardy-Weinberg equilibrium. 2. Nisha is experimenting with Daphnia for an undergraduate research project. She raises 5 generations of Daphnia in a fish tank that used to house fish for a different experiment (tank A) and others in a second tank (tank B) that has never been used before. She notices that Daphnia in tank A have large armored structures and those in tank B do not. (a) Describe an experiment that could be used to test whether this is an evolutionary response or phenotypic plasticity. (b) Nisha raises some Daphnia from tank A in tank B, and vice versa. She notices all of the Daphnia raised in tank A grow armored structures, but none in B do. Is this an example of evolutionary change or phenotypic plasticity? How can you tell? 3. The major histocompatibility complex (MHC) consists of a suite of genes that play an important role in the immune system. While studying a particular MHC locus in a population of deer found in Connecticut, you discover ample genetic variation. There appears to be two common alleles residing at this particular MHC locus. You characterize the genotype of 200 individuals from this population. You discover 40 individuals with genotype AA, 130 individuals with genotype AB, and 30 individuals with genotype BB. (a) What are the genotype frequencies of the sample population of deer? (b) What are the allele frequencies? (c) Given the allele frequencies, what are the expected Hardy-Weinberg genotype frequencies? (d) Is the population in Hardy-Weinberg equilibrium with respect to the AB MHC locus? (e) You suspect this deviation from Hardy-Weinberg equilibrium predictions could be due to non-random mating. Would you expect assortative or disassortative mating to produce this result? Explain how the non-random mating process you identified produces this pattern. (f) What allele frequencies would you predict following a generation of disassortative mating?

2 (g) What allele frequencies and genotype frequencies would you expect after a generation of random mating, assuming all of the assumptions of Hardy-Weinberg equilibrium are met? 4. Black color in horses is governed primarily by a recessive allele at the A locus. AA and Aa horses are nonblack colors, while aa horses are black all over. In the internet group rec.equestrian, one person asked why there are relatively few black horses of the Arabian breed. One response was, Black is a rare color because it is recessive. More Arabians are bay or gray because those colors are dominant. What is wrong with this explanation? (Assume that the A and a alleles are in Hardy-Weinberg equilibrium, which was probably true at the time of this discussion.) Generally, what does the Hardy- Weinberg model show us about the impact that an allele s dominance or recessiveness has on its frequency? (Modified from Freeman and Herron, 2007). 5. Scientists are studying two very different populations. The first is a laboratory population of 1,000 crickets. The genotypes at a locus coding for coloration are given below. Assume that the a allele is recessive to the A allele. AA Aa aa The second population is a pack of 10 wolves in Yellowstone National Park. The genotypes at a locus coding for coat color are given below. Assume that the b allele is recessive to the B allele. BB Bb bb While closing the crickets cage, a scientist accidently squishes a homozygous recessive individual between the lid and the cage. In a second unlucky accident, a falling tree branch kills a homozygous recessive wolf in the Yellowstone pack. Using this information, respond to parts a-c below. (a) What are the original allele frequencies and what are the new allele frequencies (after the random deaths) for the populations of wolves and crickets? (b) Which evolutionary force resulted in the differences in allele frequency? (c) Is this force stronger in the wolf or in the cricket population? Why?

3 6. In a large, randomly mating population of 1,000 daisies there are three phenotypes present: AA individuals have red flowers, Aa individuals have pink flowers, and aa individuals have white flowers. The table below gives the phenotypes of the population. Red Pink White (a) Calculate the allele and genotype frequencies. (b) If this population only self-fertilizes, what genotype frequencies would you expect after one generation of selfing? After two generations of selfing? After a hundred generations of selfing, how many pink flowers would you expect to find? 7. Consider a locus that has three alleles (A, B, and C) within a population. (a) List all of the possible genotypes. (b) Suppose that the population contains 1,000 individuals and we know 100 individuals are AA, and 50 individuals are BB. Calculate the allele and genotype frequencies for the population assuming it is in Hardy-Weinberg equilibrium. 8. [From Lecture 2 practice problems] Consider the following pair of subpopulations of a tropical butterfly, with genotype frequencies as shown: Genotype Lowland Mountain Top AA Aa aa Three biologists head to the field to collect this species, and each ends of collecting 500 individuals. The first biologist gets altitude sickness easily, so he samples only individuals from the lowlands. (a) What allele frequencies does the first biologist find (assuming he has a random sample of the population)? (b) What are the expected genotype frequencies assuming Hardy-Weinberg equilibrium? (c) How do the observed genotype frequencies compare to the expected frequencies? The second biologist hates the heat, so she drives up the mountain and samples only individuals from the top. (d) What allele frequencies does the second biologist find? (e) What are the expected genotype frequencies assuming Hardy-Weinberg equilibrium? (f) How do the observed genotype frequencies compare to the expected frequencies?

4 The third biologist is a bit more adventurous, and samples individuals continuously as she hikes up the mountain. Assume that she ends up sampling an equal number from the lowland and mountain top populations. (g) What are the observed genotype frequencies in the sample obtained by the third biologist? (h) What are the allele frequencies in this sample? (i) What are the expected genotype frequencies assuming Hardy-Weinberg equilibrium? (j) Which genotype(s) is overrepresented in the observed sample compared to the expected sample? Which is underrepresented? (k)what would the third biologist conclude about Hardy-Weinberg equilibrium? (l) What assumption that we used in deriving the Hardy-Weinberg equilibrium is violated in this case? 9. It is estimated that every individual human carries 3-5 recessive lethal alleles (i.e. alleles that cause death in the homozygous state) in their genome of about 30,000 loci. Use this information and what you know about the effects of inbreeding to explain the observation that inbred individuals (of many species) are on average less likely to survive than individuals that result from random matings. 10. Collared lizards in the eastern Ozarks used to be widespread, but now occur in remnant habitat patches isolated by dense forest. For each of the following scenarios (ae, below), draw a bar graph showing the expected number of populations (out of 100) on the Y axis versus the allele frequency for the given allele on the X axis 1000 generations after habitat fragmentation. Suggestion: Think about whether or not you expect fixation to have occurred in each case, and how much divergence you expect among populations. Initial allele frequency Migration rate Effective population size a b c ,000 d

5 11. A new allele arises in a single individual in a population of 50 diploid individuals. Assuming this new allele has no affect on survival or fecundity, what is the probability that this allele becomes fixed in the population? 12. [Not covered until lecture Thursday 2/5] Populations of sand lizards (Uma notata) live in large, isolated sand dunes in the southwestern United States. Herpetologists studying these lizards in Imperial County, California found that the frequency of the Fringe-toed allele was 0.88 in an eastern dune population and only 0.12 in a western dune population. Suppose that a brutal windstorm comes along and blows enough sand around to create a corridor in which some of these lizards can boldly migrate from the eastern dune to the western dune. After the storm is over, 279 individuals are collected from the western dune, 37 of which are from the eastern dune in the last generation. (a) Calculate the migration rate into the western dune. (b) What would the frequency of the Fringe-toed allele be in the western sand dune after one generation of migration? (c) Use this example to explain why a population experiencing migration is NOT in Hardy-Weinberg equilibrium.